The high-throughput yeast deletion fitness data and the theories of dominance

Journal of Evolutionary Biology

Volumn 25, Issue 5, 2012, Pages 892-903

  Manna, F ^a   Gallet, R ^a   Martin, G ^b   Lenormand, T ^a  

^a CENTRE D ECOLOGIE FONCTIONNELLE ET EVOLUTIVE   (France)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

Author keywords

Density kernel; Measurement error; Mutation of small and large effect; Yeast deletion database

Indexed keywords

FUNGAL DNA;

CORRELATION; DATA SET; DATABASE; DOMINANCE; EXPERIMENTAL STUDY; FITNESS; HETEROZYGOSITY; MEASUREMENT METHOD; MUTATION; YEAST;

ARTICLE; BIOLOGY; DOMINANT GENE; FUNGAL GENE; GENE DELETION; GENETIC DATABASE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HOMOZYGOTE; METHODOLOGY; REPRODUCIBILITY; REPRODUCTIVE FITNESS; STATISTICAL MODEL; TIME; TOMOGRAPHY; YEAST;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA, FUNGAL; GENES, DOMINANT; GENES, FUNGAL; GENETIC FITNESS; HETEROZYGOTE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOMOZYGOTE; LINEAR MODELS; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SEQUENCE DELETION; TIME FACTORS; TOMOGRAPHY; YEASTS;

EID: 84859451172     PISSN: 1010061X     EISSN: 14209101     Source Type: Journal    
DOI: 10.1111/j.1420-9101.2012.02483.x     Document Type: Article

References (25)

1. Agrawal, A.F. & Whitlock, M.C. 2011. Inferences about the distribution of dominance drawn from yeast gene knockout data. Genetics 187: 553-U274.
2. Bourguet, D. 1999. The evolution of dominance. Heredity 83: 1-4.
3. Bürger, R. & Bagheri, H. 2008. Dominance and its evolution. In: Encyclopedia of Ecology (S.E. Jørgensen & B.D. Fath, eds), pp. 945-952. Elsevier, Oxford.
4. Charlesworth, B. 1979. Evidence against Fisher's theory of dominance. Nature 278: 848-849.
5. Crow, J.F. & Abrahamson, S. 1997. Seventy years ago: mutation becomes experimental - H. J. Muller. Genetics 147: 1491-1496.
6. Elena, S.F., Ekunwe, L., Hajela, N., Oden, S.A. & Lenski, R.E. 1998. Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102-3: 349-358.
7. -3: method, questions and prospects. Genetics 190: 175-186.
8. Gu, Z.L., Steinmetz, L.M., Gu, X., Scharfe, C., Davis, R.W. & Li, W.H. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
9. Han, J., Kamber, M. & Pei, J. 2012. Data Mining. Concepts and Techniques, 3rd edn. Elsevier, Oxford.
10. Hansen, T.F. 1992. Selection in asexual populations - an extension of the fundamental theorem. J. Theor. Biol. 155: 537-544.
11. Houle, D., Govindaraju, D.R. & Omholt, S. 2010. Phenomics: the next challenge. Nat. Rev. Genet. 11: 855-866.
12. Hughes, T.R., Roberts, C.J., Dai, H.Y., Jones, A.R., Meyer, M.R., Slade, D. et al. 2000. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet. 25: 333-337.
13. Lynch, M. & Walsh, B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland.
14. Manna, F., Martin, G. & Lenormand, T. 2011. Fitness landscape: an alternative theory for the dominance of mutations. Genetics 189: 923-937.
15. Mayo, O. & Burger, R. 1997. The evolution of dominance: a theory whose time has passed? Biol. Rev. Camb. Philos. Soc. 72: 97-110.
16. Mukai, T. 1964. The genetic structure of natural population of Drosophila melanogaster. I. Spontaneous mutation rate of polygenes controlling viability. Genetics 50: 1-19.
17. Phadnis, N. & Fry, J.D. 2005. Widespread correlations between dominance and homozygous effects of mutations: implications for theories of dominance. Genetics 171: 385-392.
18. Shoemaker, D., Lashkari, D., Morris, D., Mittmann, M. & Davis, R. 1996. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14: 450-456.
19. Silverman, B. 1986. Density Estimation for Statistics and Data Analysis. Chapman and Hall, London.
20. Simmons, M.J. & Crow, J.F. 1977. Mutations affecting fitness in Drosophila populations. Annu. Rev. Genet. 11: 49-78.
21. Smith, A.M., Heisler, L.E., Mellor, J., Kaper, F., Thompson, M.J., Chee, M. et al. 2009. Quantitative phenotyping via deep barcode sequencing. Genome Res. 19: 1836-1842.
22. Steinmetz, L.M., Scharfe, C., Deutschbauer, A.M., Mokranjac, D., Herman, Z.S., Jones, T. et al. 2002. Systematic screen for human disease genes in yeast. Nat. Genet. 31: 400-404.
23. Szafraniec, K., Wloch, D.M., Sliwa, P., Borts, R.H. & Korona, R. 2003. Small fitness effects and weak genetic interactions between deleterious mutations in heterozygous loci of the yeast Saccharomyces cerevisiae. Genet. Res. 82: 19-31.
24. Wagner, A. 2000. Robustness against mutations in genetic networks of yeast. Nat. Genet. 24: 355-361.
25. Winzeler, E.A., Shoemaker, D.D., Astromoff, A., Liang, H., Anderson, K., Andre, B. et al. 1999. Functional characterization of the S-cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.